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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:23, 17 September 2013


Full id: C457_salivary_Prostate_oral_Small_Keratinocyte_Urothelial_Mammary



Phase1 CAGE Peaks

Hg19::chr6:56480719..56480734,-p@chr6:56480719..56480734
-
Hg19::chr6:56483141..56483154,-p@chr6:56483141..56483154
-
Hg19::chr6:56483724..56483742,-p57@DST
Hg19::chr6:56483961..56483984,-p33@DST
Hg19::chr6:56484092..56484104,-p63@DST
Hg19::chr6:56484207..56484218,-p79@DST
Hg19::chr6:56484346..56484362,-p29@DST
Hg19::chr6:56484382..56484393,-p76@DST
Hg19::chr6:56484469..56484489,-p38@DST
Hg19::chr6:56484495..56484517,-p31@DST
Hg19::chr6:56484521..56484552,-p23@DST
Hg19::chr6:56484616..56484636,-p@chr6:56484616..56484636
-
Hg19::chr6:56484716..56484736,-p@chr6:56484716..56484736
-
Hg19::chr6:56484743..56484754,-p@chr6:56484743..56484754
-
Hg19::chr6:56484773..56484794,-p@chr6:56484773..56484794
-
Hg19::chr6:56484963..56484989,+p@chr6:56484963..56484989
+
Hg19::chr6:56485093..56485108,-p@chr6:56485093..56485108
-
Hg19::chr6:56485129..56485140,-p@chr6:56485129..56485140
-
Hg19::chr6:56485148..56485166,-p@chr6:56485148..56485166
-
Hg19::chr6:56485169..56485189,-p@chr6:56485169..56485189
-
Hg19::chr6:56485258..56485269,-p@chr6:56485258..56485269
-
Hg19::chr6:56485473..56485485,-p@chr6:56485473..56485485
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.82e-14253
endo-epithelial cell7.37e-1442
endodermal cell4.24e-1258
epithelial cell of alimentary canal1.70e-1120
squamous epithelial cell5.16e-0763
Uber Anatomy
Ontology termp-valuen
orifice4.14e-1136
oral opening5.68e-1022
endoderm-derived structure8.60e-10160
endoderm8.60e-10160
presumptive endoderm8.60e-10160
respiratory system9.23e-1074
mouth mucosa8.01e-0913
mouth4.92e-0829
stomodeum4.92e-0829
digestive system9.13e-08145
digestive tract9.13e-08145
primitive gut9.13e-08145
surface structure1.46e-0799
mucosa of oral region2.36e-074
respiratory system mucosa2.36e-074
ectoderm-derived structure7.77e-07171
ectoderm7.77e-07171
presumptive ectoderm7.77e-07171
Disease
Ontology termp-valuen
squamous cell carcinoma2.78e-1714
carcinoma1.24e-12106
cell type cancer2.49e-11143
cancer9.89e-09235
disease of cellular proliferation3.13e-08239


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.47965e-08
MA0004.10.158412
MA0006.10.0694838
MA0007.11.41691
MA0009.10.526253
MA0014.10.00310052
MA0017.10.0884918
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.12.96491
MA0042.10.894828
MA0043.10.526535
MA0046.10.516541
MA0048.10.0283321
MA0050.13.53975
MA0051.12.62489
MA0052.10.459414
MA0055.10.0249719
MA0056.10
MA0057.10.00450362
MA0058.10.101748
MA0059.10.101051
MA0060.10.0258987
MA0061.10.0189504
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.0112936
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.13.42403e-11
MA0074.12.62111
MA0076.10.110503
MA0077.10.49237
MA0078.12.25524
MA0081.10.679272
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.00120138
MA0089.10
MA0090.10.378129
MA0091.10.160096
MA0092.10.4236
MA0093.10.0708814
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.0724124
MA0103.10.0653004
MA0105.10.00342752
MA0106.10.259598
MA0107.10.041912
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.74833
MA0114.10.0401034
MA0115.10.747865
MA0116.10.0431675
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.234116
MA0139.10.0162019
MA0140.11.09628
MA0141.11.64549
MA0142.10.359701
MA0143.10.272236
MA0144.10.328518
MA0145.10.00165086
MA0146.10.00599554
MA0147.10.0444528
MA0148.10.174705
MA0149.10.192747
MA0062.20.0177333
MA0035.22.43482
MA0039.25.36166e-08
MA0138.20.302079
MA0002.21.0893
MA0137.20.578057
MA0104.20.0256869
MA0047.20.250458
MA0112.20.00138028
MA0065.20.00177701
MA0150.10.115337
MA0151.10
MA0152.10.589582
MA0153.10.615584
MA0154.10.0194777
MA0155.10.00116092
MA0156.10.0812668
MA0157.10.337287
MA0158.10
MA0159.11.06197
MA0160.10.543697
MA0161.10
MA0162.15.0328e-05
MA0163.11.468e-05
MA0164.10.28168
MA0080.20.248589
MA0018.20.260646
MA0099.20.204301
MA0079.20
MA0102.22.35918
MA0258.10.032189
MA0259.10.0476147
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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